rs7241142

Variant names:

• chr18-894241-G-A
• rs7241142
• ENST00000717225.1:n.716C>T

Your query was ambiguous. Multiple possible variants found:

• chr18-894241-G-A
• chr18-894241-G-C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000717225.1(ENSG00000265179):​n.716C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.618 in 151,976 control chromosomes in the GnomAD database, including 31,076 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.62 (31076 hom., cov: 31)
• Consequence: ENSG00000265179 ENST00000717225.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.26
• Publications: 2 publications found

Genes affected

ENSG00000265179 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.764 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000265179	ENST00000717225.1	n.716C>T		non_coding_transcript_exon_variant	Exon 2 of 2
ENSG00000265179	ENST00000582554.2	n.*186C>T		downstream_gene_variant		5
ENSG00000265179	ENST00000717226.1	n.*188C>T		downstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.618 AC: 93894 AN: 151858 Hom.: 31073 Cov.: 31

Gnomad AFR AF: 0.363

Gnomad AMI AF: 0.715

Gnomad AMR AF: 0.718

Gnomad ASJ AF: 0.714

Gnomad EAS AF: 0.784

Gnomad SAS AF: 0.768

Gnomad FIN AF: 0.660

Gnomad MID AF: 0.693

Gnomad NFE AF: 0.714

Gnomad OTH AF: 0.646

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.618 AC: 93925 AN: 151976 Hom.: 31076 Cov.: 31 AF XY: 0.621 AC XY: 46152 AN XY: 74276

African (AFR) AF: 0.363 AC: 15037 AN: 41428

American (AMR) AF: 0.717 AC: 10961 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.714 AC: 2476 AN: 3470

East Asian (EAS) AF: 0.784 AC: 4049 AN: 5162

South Asian (SAS) AF: 0.769 AC: 3703 AN: 4814

European-Finnish (FIN) AF: 0.660 AC: 6958 AN: 10544

Middle Eastern (MID) AF: 0.694 AC: 204 AN: 294

European-Non Finnish (NFE) AF: 0.714 AC: 48520 AN: 67968

Other (OTH) AF: 0.649 AC: 1366 AN: 2106

Alfa AF: 0.655 Hom.: 5932

Bravo AF: 0.610

Asia WGS AF: 0.734 AC: 2552 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.11
DANN	Benign	0.28
PhyloP100		-1.3

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs7241142; hg19: chr18-894242;